bb86c0e03a
Improved error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:43:13 +00:00
68719615be
For multiple matches, shifted counter to be 1-based
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3370 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:41:50 +00:00
73e2e32837
Fix typo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3369 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:04:00 +00:00
ebd0fabf86
First pass updates to annotations to work with indels. HomopolymerRun indel behavior is currently turned off by a global boolean until it's ready to go live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3368 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:02:13 +00:00
0791beab8f
Checking in downsampling iterator alongside LocusIteratorByState, and removing
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the reference implementation. Also implemented a heap size monitor that can
be used to programmatically report the current heap size.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3367 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:00:44 +00:00
b7d21627ab
Changes to DepthOfCoverage (JIRA items) and added back an integration test to cover it. Alterations to the design file generator to output all transcripts (rather than choosing one at random).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3366 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 17:23:00 +00:00
4235164359
Removed the confusionMatrix column (of *course* this is a confusion matrix... what else would it be?!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3365 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 21:55:37 +00:00
95b29f608b
Specify default values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3364 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 21:42:53 +00:00
6efd05831b
Encapsulating annotation decoding function in order to use same fixed random seed in both VariantOptimizer and ApplyVariantClusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3363 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 20:03:38 +00:00
32389dc0a9
Fixed GQ estimate when chosen genotype isn't the most likely according to the GLs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3362 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 19:17:46 +00:00
1538dc0144
optimizer now uses -an arguments instead of exclude and force for clarity. command-line length reduced by 50%
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3361 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 15:41:44 +00:00
88bd7a2045
Reenabling UG parallelization performance tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3360 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 16:28:08 +00:00
0490909285
Fixed epic generic paths fail.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3359 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 15:59:57 +00:00
7ef87e5126
An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less
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than a minute and fell over instantly in the case of the Tribble parallelism issue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 15:40:43 +00:00
ceec525420
Got rid of stray unicode characters in copyright message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3357 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 14:47:39 +00:00
3e9ad4bbd0
Porting SAM pileup ROD to Tribble as a case study.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3356 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 00:22:59 +00:00
6839c194cb
although holding on to memories can be fun, it's bound to hurt performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3355 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 19:26:58 +00:00
c81b910f73
Commenting out the parallelization test which is failing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3354 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 18:39:53 +00:00
cac98ba5ef
a couple of small documentation fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 17:40:27 +00:00
3f07611187
Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3350 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 13:36:31 +00:00
2c55ac1374
fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 06:13:26 +00:00
6868ce988f
Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an
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indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 17:31:19 +00:00
34969f304c
Adding dbsnp to all UG performance tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3347 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 15:48:05 +00:00
140e43b93b
Checking in to see whether it fails. If I start getting bombarded with Bamboo error reports, I'm commenting it out...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3346 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 15:39:42 +00:00
572b383fe2
Make VA annotate dbsnp again
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 14:06:53 +00:00
b09e7231d1
A quick implementation of the experimental covariates for the TGen folks to work with.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 01:08:52 +00:00
aec5f7b630
Can now threshold results based on minimum base and/or mapping quality.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3343 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 19:58:07 +00:00
13fd182b7c
For dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 15:17:05 +00:00
4a7902bb8e
Bases 'A' and 'a' (etc.) no longer considered different.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:53:38 +00:00
ec543b7b62
The Complete Genomics confusion matrix rates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3338 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:52:10 +00:00
b223b04331
Don't list '.' as an alternate allele, dummy!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3337 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:51:18 +00:00
98718d0faa
Computes the error rate per cycle
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3336 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:50:22 +00:00
7527f950d1
Computes the quality score distribution per readgroup (one column per readgroup)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3335 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:49:38 +00:00
c111c15072
Computes the distribution of insert size per library (for now, one output file per library)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3334 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:48:35 +00:00
a51bd57566
First version of the smart batch merging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3333 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 02:18:48 +00:00
33a9549896
Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3332 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-09 16:48:07 +00:00
76efa757f0
Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder
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which improved startup time 5-10x when dynamically merging many BAMs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-08 14:12:22 +00:00
504103bd15
Misc. additions to correct utilities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:34:18 +00:00
64ccaa4c6a
Walkers and integration tests that calculate and compare callable bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3328 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:33:47 +00:00
d070554329
A walker that calculates read lengths, number and size of clipping events
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3327 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:32:51 +00:00
1749a49042
Mapping and base quality thresholds for DoC default to none
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 18:08:13 +00:00
7d2df3f511
example windowed ROD walker for Kristian, and updates to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 17:12:50 +00:00
57f254b13a
VE integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3324 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:58:25 +00:00
44de92e09d
Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 12:31:56 +00:00
18f1d31a22
Moving to and organizing in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 04:05:36 +00:00
06ea65e60b
again for JIRA GSA-320
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3319 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 03:47:58 +00:00
ac9b32db88
a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3318 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 03:31:43 +00:00
4e0019b04f
Repair code that sorts and merges intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:37:25 +00:00
72e030a670
require that snps be biallelic before we pass them to the TiTv calculation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:33:00 +00:00
7cecec7d00
Removing zero no-calls restriction in AC stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3314 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:55:07 +00:00
0e58fb7cc0
Moved over to be a walker inside the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:28:03 +00:00
78409dca0d
turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 16:36:58 +00:00
bacc507a48
Don't worry about sorting anymore in the liftover tool. That will come later.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3311 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 15:00:30 +00:00
5df0361bd2
trivial removal of unnecessary comments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3309 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:51:14 +00:00
2975e3a4e8
picard Intervals don't sort right - switching to GenomeLocs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3308 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:50:28 +00:00
1a99fb9318
First pass at liftover tool. Passing buck over to Aaron...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:38:19 +00:00
a0d71540df
speed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3305 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:19:42 +00:00
6bbcc47b5d
removing some out-of-date RODs and some unused genotype writer formats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 19:07:13 +00:00
c998c48a23
adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3303 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:55:36 +00:00
a68f3b2e9c
VCF moved over to tribble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3302 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:28:48 +00:00
ad11201235
adding more ROD pile-up tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3301 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 16:01:11 +00:00
0338345bee
Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 15:42:27 +00:00
64640d6b17
Complete the switch statement to deal with all possible cigar operators for Kris.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 13:41:05 +00:00
f75e54e3f7
fixes for new package names in tribble 74
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:47:04 +00:00
617542853f
Walker that can be used with refGene and a TCGA bed file to annotate intervals in an interval list with the genes and exons they overlap.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3296 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:55:01 +00:00
354262eabe
New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:54:18 +00:00
03bea70f3a
Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-04 16:49:21 +00:00
510b3efcc2
Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3292 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 18:46:33 +00:00
94b51de401
HLA caller updated to examine class II loci, updated pointers to dictionary, allele frequencies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3290 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 14:54:52 +00:00
97fdd92e7b
Clean up the code to have a unified approach to calculating p(true) for both with and without ti/tv models
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3289 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 13:30:20 +00:00
f497213933
DbSNP moved over to tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 06:02:35 +00:00
9d01670f62
Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3286 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-02 19:21:23 +00:00
a318b1871d
Removed unused column
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3285 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 21:29:34 +00:00
9dff578706
Added PG tag to bam header to let people know it's been cleaned.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
0e10359a5e
Okay, finished up the ability to cap a base's qual by its read's mapping quality.
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This is experimental - I have not tested its performance on SNP calling, or even played around with it. If you want to test it out, go nuts. But don't come running to me if your results are not good.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:58:30 +00:00
850f36aa61
Changes to the Unified Genotyper's arguments:
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1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:44:24 +00:00
8b2ce128b5
Optimized the join(..) method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3280 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:55:07 +00:00
8bb15ef812
Checking in the reference implementation of the downsampler for back comparison.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:41:13 +00:00
1714c322c2
Reorg of UG args; checking in first before upcoming changes that will break integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 14:48:46 +00:00
ba78d146ec
Finished implementing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3273 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 14:14:31 +00:00
5d5c7f9d34
Changed short code of stop codon to 'stop'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3272 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 13:55:52 +00:00
cbed0b1ade
Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 22:50:17 +00:00
7fbfd34315
adding the GELI ROD validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3270 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 21:43:00 +00:00
82818a417b
Allow header fields to come in any order...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3269 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 18:33:10 +00:00
4617abf1ff
Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 20:42:04 +00:00
e2ff4167af
Added "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3266 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 18:38:33 +00:00
5dce16a8f1
Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 13:10:11 +00:00
64c5f287c5
fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3264 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 17:46:46 +00:00
c647153b10
Adding Jama for Ryan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 14:30:36 +00:00
f6468f9143
a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3261 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 04:49:49 +00:00
df31eeff9f
minor change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3259 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 06:05:29 +00:00
68bdac254b
a utility walker for validating changes made to the underlying ROD system in the transistion to Tribble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3258 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:21:24 +00:00
d9bf441391
Have UG emit calls at sites from one or more 'trigger' tracks when provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3257 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:04:43 +00:00
8f2bfac7a6
Bug fix for NullPointerException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3256 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:02:09 +00:00
f5a3b128c8
Fixing bug that's not caught by integration tests:
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If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics. Instead, just check that any eval's no-call count is 0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3255 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 02:40:34 +00:00
29ab59a7b3
Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-24 21:31:03 +00:00
c8d09a29ed
some quick changes to the VE output system - more to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3253 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 21:55:08 +00:00
7f4d5d9973
Ti/Tv by AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 17:56:29 +00:00
42bcca1010
Pulling out the left-alignment code for indels so that other walkers can use it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 16:12:34 +00:00
9e28e4eb42
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3250 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:50:09 +00:00
10bcd72593
1st attempt to implement extra columns
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3249 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:49:37 +00:00
a72a5a7b1a
Data object for representing a single amino acid
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3248 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:49:06 +00:00
e7c0ded40e
Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:48:41 +00:00
e0b51d0df0
Trigger cleaning of duplicate reads. Also beeter debug output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:12:28 +00:00
3adf7fbf64
bug fix for known-indels used as consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 13:52:51 +00:00
f050beada6
make sure we do delete the temp file we create
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3244 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:32:49 +00:00
536f22f3bd
adding VC adaptor for GELI, along with unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:28:39 +00:00
3d2c836db6
Bug fix for case sensitivity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3242 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 03:08:58 +00:00
8c94df6f00
Bug fix for Chris: deal with sites that have "semi-deletions"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3241 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 18:34:41 +00:00
121163dd49
interim commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3240 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 13:44:45 +00:00
f0fe2ea530
A simple codon -> AA lookup table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3239 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 12:18:00 +00:00
e643a9e7a5
Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3238 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 12:11:19 +00:00
653e08c0b6
Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3237 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 12:11:03 +00:00
20379c3f82
Added location-caching optimization, temporary attributes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3236 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 11:35:45 +00:00
84ebceb9a6
Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 02:05:10 +00:00
e7334ec11f
Checkin for Eric (IndelDBRateWalker is a prelude to a VariantEval module for comparisons for indels)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3234 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 00:40:27 +00:00
32d86cf457
Rev the reservoir downsampler to support partitioning through a functor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3232 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:50:26 +00:00
ef6d900eb8
for now, set log error to -1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3231 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:21:06 +00:00
e9e844fbf5
1. Reverting: dbsnp automatically is a comp
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2. Fixing logic for min Qscore calculation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:51:35 +00:00
532263ea25
Oooops, forgot to update the test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3229 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:38:24 +00:00
1373fee278
Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change.
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VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument.
SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:19:03 +00:00
ab34397d2e
Continuing to stamp out the non-ASCII copyright virus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3227 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 14:50:45 +00:00
84f1ccd6ac
Two dumb oneoff walkers written to fix & annotate the Baylor indel calls (which came in sans reference, and without coding/intron annotations).
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ERIC -- does the IndelAnnotator (the RefSeq lookup code I stole from IndelGentoyperV2) want to be its own Annotation inside VariantAnnotator? Is Andrey already doing this as part of adding indel calling to UG?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3226 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 14:04:10 +00:00
2fdc1cf490
Bed ROD track support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:42 +00:00
51b3998082
deleting unused code from VariationFiltration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3224 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:19 +00:00
4abd3b0b7b
Fixing known/novel calc now that dbsnp isn't a default comp track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:43:59 +00:00
114819d980
Allow user to set min confidence score for comp tracks too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:09:09 +00:00
3db73e0791
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 03:00:43 +00:00
3b5673d967
1. Removed -all; by default all modules are used; use -none for no modules.
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2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 02:46:42 +00:00
4e18c54bb8
fixing a couple of commented out portions of the VCFReader test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3219 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 22:20:35 +00:00
6fda78f93f
Always return deleted bases in upper case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3218 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 19:17:40 +00:00
52a570637d
Always keep event bases in upper case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3217 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 19:16:39 +00:00
80c4f88a72
removing the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:56:45 +00:00
7d952a34ae
Fixing copyright note
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3215 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:28:57 +00:00
cdc175f7e3
Synchronizing version to make sure everything compiles; this model is not operational yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3214 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:41:52 +00:00
4437456bb5
Pass array of ref bases to callExtendedLocus()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3213 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:41:13 +00:00
5d2fab93f4
Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:40:30 +00:00
01e6492ba9
Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3211 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:38:09 +00:00
4723cad1be
New method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase())
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3210 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:35:09 +00:00
cac125b35c
Fixed incorrect symbol printed into the output file (tag had 'R', should have had 'T')
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:37:28 +00:00
f4977965b6
Removing debug statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3208 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:22:40 +00:00
124b7a2a58
Moved ApplyVariantClusters over to VariationContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3207 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:20:25 +00:00
200d3e2c47
added copyright note
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3205 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:44:26 +00:00
546dfb629e
A draft (working) version of a tool that computes per-cycle base qualities averaged across the reads; the computed base qual profiles are stratifeid by lane/read end and separately by library.Come and shoot me if we already have such a tool somewhere in the repository :)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3204 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:38:16 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
b5f6f54968
Almost done removing any trace of the old Variation and Genotype interfaces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 14:52:15 +00:00
818a95ea6e
Test of new copyright message without unicode characters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3200 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 14:14:54 +00:00
00feb3eee0
Moving over to VariationContext in CountCovariates. Removed references to class Variation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3199 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 13:26:22 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
c08936d6f4
Added a reservoir downsampler which can sample elements in an iterator uniformly
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from a stream (see Vitter 1985). Thanks to Eric and Andrey for the pointer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3197 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 20:48:14 +00:00
c44f63c846
Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3196 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 14:28:12 +00:00
abf48cee05
Moving over to VariantContext from Variation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3195 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 06:56:29 +00:00
d73c63a99a
Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.
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Also, adding some more useful integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 05:47:17 +00:00
131703d9db
more clean-up: moving AlleleBalanceInspector to archive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3192 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 20:53:33 +00:00
534f24177a
Move to VariantContext and improve performance (and ease of use) by transitioning to be a RODWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3191 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 20:09:48 +00:00
8c32bb8f0a
Complete the move over to VariantContext so that we can remove dependence on Variation (in the VCF code)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3190 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 19:41:42 +00:00
821e8b1c5f
more cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3189 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 19:16:16 +00:00
e11ca74eb5
removing some outdated ROD classes (PooledEMSNPROD and SangerSNPROD), removing an out-of-date interface (VariantBackedByBenotype), and moving AnalyzeAnnotationWalker over to VariationContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3188 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 18:59:29 +00:00
d5e5589b8f
No longer used
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3187 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 17:57:39 +00:00
be7cbf948b
adding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3186 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 17:41:48 +00:00
4d75b26b7a
Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 06:17:31 +00:00
6dc1275cfb
Utility method added: getQualsInCycleOrder(read) - examines the read and returns its quals in the order the machine read them (i.e. always from cycle 1 to cycle N). Simply inverts quals if the read happens to be rc-aligned :)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3183 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 00:15:57 +00:00
f4673efd2f
Moving to archive as it's no longer supported
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3182 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:10:42 +00:00
02a6f4c401
Moving over to VariantContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:07:28 +00:00
7adff5b81a
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:36:19 +00:00
e702bea99f
Moving VE2 to core; calling it "VariantEval" (one more checkin coming)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:25:47 +00:00
ac6f6363ce
Execs() temporarily disabled after removal of bam file. New tests forthcoming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3178 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:11:56 +00:00
ac9dc0b4b4
Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:53:02 +00:00
3330e254a9
Standardize the dbsnp track name in preparation for case-sensitivity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:41:57 +00:00
5f7564bf0a
Better naming of output columns
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 18:08:07 +00:00
e682460c1f
add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 16:31:43 +00:00
b54031fc86
adding an experimental format to VariantEval2, which when you source() from R, imports all VE2 output as individual tables with appropriate row and column names. More testing and feedback needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3172 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 06:09:27 +00:00
04909fa6ad
Removing arbitrary selects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 17:46:39 +00:00
f1189bac5a
Bug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3168 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 16:58:55 +00:00
b930dc52a5
Integration test for GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3167 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:43:25 +00:00
c0f4695902
Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3166 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:42:19 +00:00
74ec72d1ac
Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3164 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:39:50 +00:00
77a6608784
Changed a variable name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3163 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:38:18 +00:00
7b8056099c
Fixed 'N' reference-base handling, changed some comments, var names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3162 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:37:25 +00:00
dde092fb61
Added the ability in VE2 to select which eval modules to run, so that you aren't forced to use all of them. You can use --list to list all of the possible modules to run.
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Heads up everyone: by default, *no* modules are run. Please add "-all" to your scripts to maintain the previous behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3161 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 22:15:58 +00:00
0b575596f8
Fix for concordance: samples found only in truth no longer kill it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 21:33:49 +00:00
8573b0bc6f
Refactoring intervals, separating the process of parsing interval lists,
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sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:50:38 +00:00
d0123956bc
Modified comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3158 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:41:59 +00:00
7b05091c04
DoC now does not require a -o argument. (Change for Matt)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 13:58:17 +00:00
e413882302
Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 20:42:18 +00:00
14b8101d45
Error message fail. Failed to supply one of the valid interval file types.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3153 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 01:19:01 +00:00
60d54e69f3
Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 01:11:27 +00:00
d06c7835d8
Adding performance tests for the indel realigner; should take ~3 hours.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 04:45:22 +00:00
3434a61146
Don't trigger when ref=N (which can happen when a dbsnp track is provided)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 02:59:11 +00:00
961ca05abc
Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 01:43:07 +00:00
fa01876255
UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 19:42:29 +00:00
0cc6d0fbbb
One more quick memory improvement: reuse Alleles in a given context instead of creating new ones for each sample (duh).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3147 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:48:36 +00:00
c2a37e4b5c
Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3146 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:36:06 +00:00
71f38a9199
Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).
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Should take ~3 hours to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:30:59 +00:00
e73e6a4fb0
Significant memory improvements to plink code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3144 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 16:12:38 +00:00
f1b1e70612
Bug fix for multisample calls in ApplyVariantClusterWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 12:01:15 +00:00
3f2455e346
Better error message as suggested by James P
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:52:53 +00:00
fba48b515a
Heads up everyone:
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For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:37:25 +00:00
e286623f6f
Use byte[] instead of String in an attempt to cut down on memory usage
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3139 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:32:54 +00:00
7025f5b51d
Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 19:37:17 +00:00
9f6377f7fb
added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval.
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 15:37:15 +00:00
4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
e148a3ac61
added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option.
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Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.
WARNING: for very large ROD's this can be costly. Consider this experimental for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 05:14:41 +00:00
20cc2a85a4
removed the hashmap from Genotype Concordance, moved it into a table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 21:24:48 +00:00
e55f27b3b1
forgot a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3132 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:51:13 +00:00
9ca8e345fc
by-by old junk.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3131 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:41:48 +00:00
8fd59c8823
Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:39:55 +00:00
918b746798
More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3129 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 16:38:28 +00:00
e7dad728df
Trivial output changes for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 14:47:43 +00:00
058e7d3d12
Bug fix for Gregory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3127 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 00:21:35 +00:00
7b44e6bd55
ApplyVariantClusters now outputs interesting threshold points based on hitting the target novel TiTv
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3126 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 19:47:29 +00:00
60c227d67f
Added new VE2 module to create a plot of titv ratio by variant quality score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3125 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:19:27 +00:00
3530ef5a41
Explicit type cast fixed in order to work with new ROD implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:02:56 +00:00
2d002c56c3
Added histogram of variant quality scores broken out by true positive and false positive calls to the GenotypeConcordance module of VariantEval2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3123 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 13:48:31 +00:00
12e4f88ca7
a little bit more clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3122 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-05 20:49:06 +00:00
df7e7921ce
removing some unused code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-05 19:30:08 +00:00
56eb15f91f
Error checking for bad input (thanks, Aaron).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3120 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-04 03:17:01 +00:00
705b28e90d
First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3118 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 21:52:26 +00:00
d78e7f6c0a
Added documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3117 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 21:51:28 +00:00
8017fb123f
changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 20:55:19 +00:00
6b7b07f178
First checkin of GenomicAnnotator which annotates an input VCF file by pulling data in a generic way from an arbitrary set of TabularRODs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3114 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 17:49:42 +00:00
642c969896
reverting optimizer changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3112 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 16:59:13 +00:00
d7880ef7ad
Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3110 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 17:17:16 +00:00
f7d1b8f5de
CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.
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Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:27:23 +00:00
585cc880a2
changed jexl expressions to jexl names in the VariantEval2 output, fixed integration test, and fixed a problem where a line was getting dropped in CSV output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3108 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:23:14 +00:00
d00bde22db
Reverting one of Brett's changes that should not have been committed. Will
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address with Brett separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3107 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:10:46 +00:00
b4f6f54502
Reorganizing the way interval arguments are processed
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Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java:
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java
New restrictions:
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 12:47:48 +00:00
c3c6e632d1
support for two new VCF header info field value-types, Flag (for fields that are just boolean truths), and Character (for single charatcer info fields).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3105 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 03:11:32 +00:00
3d3d19a6a7
the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.
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a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 22:39:56 +00:00
4fcee248f9
For Kristian: functions which, given a read, can uniquely identify the BAM file storing that read.
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Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3103 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 20:46:44 +00:00
d58fe70708
Correctly ignore filtered calls and indel calls in the truth sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3101 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 14:33:01 +00:00
b60197ae10
Another round of cleanup and simplification in Picard -- Picard's unit tests
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are now passing for my branch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3100 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 01:02:59 +00:00
40f8e7644c
Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3099 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 23:57:36 +00:00
f992f51a3b
Deleting incorrect sampling genotype likelihoods from the codebase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3098 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 23:56:35 +00:00
b9d3fc3fbb
Now checks if the i-th element of the FiltrationContext[] is null before trying to access it. This seems to happen occassionally at the very end of a VCF file... the array will be 6 elements long, but the last element will actually be null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3097 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 22:40:17 +00:00
400684542c
Revisions to take into account finalization of Picard patch: naming changes, better definition
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of public interfaces. This won't be the last Picard patch, but it should be the last big one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 19:28:14 +00:00
b00d2bf2bc
fixing an annotation that was breaking the error log output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3095 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 15:34:04 +00:00
a6e8687d71
implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3094 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 04:20:19 +00:00
babb9fb825
snp cluster filter should ignore ref calls when determining the clusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 17:57:33 +00:00
24461a2503
Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3091 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:59:01 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
1e8b3ca6ba
Fare thee well, oh LocusWindowTraversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:17:26 +00:00
8ea98faf47
Deleting the pooled calcluation model -- no longer supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 11:44:27 +00:00
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
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Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 03:21:27 +00:00
a45ac220aa
Removing unnecessary printing routines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 22:34:54 +00:00
b8ab74a6dc
Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3085 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 21:45:22 +00:00
e9e53f68ab
Filter lists can now end with .list or .txt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3084 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 17:41:24 +00:00
074ec77dcc
First go of the new output system for VE2. There are three different report types supported right now (Table, Grep, CSV), which can be
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specified with the reportType command line option in VE2.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3083 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 03:59:32 +00:00
85f4f66180
Updated to use VariantContext. Output has been reformatted: variant and genotype concordance are emitted for every coverage level per variant. If the requested sampling level is higher than what's available, the maximum available coverage at that locus is used. This makes it much easier to make plots indicating the percentage of comparison callset recovered at a certain sampling depth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3082 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 21:02:43 +00:00
391e5843e4
If the annotation engine has not been supplied, don't try to annotate anything.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 20:52:21 +00:00
weisburd
hanna
chartl
kiran
rpoplin
ebanks
depristo
aaron
asivache
sjia
bthomas
kshakir